Comparative genomic hybridization (CGH) has demonstrated its ability to screen the entire genome and provide a unique insight into the gains and losses of DNA sequence that are involved in the development of cancer. In CGH total genomic DNAs from a tumor and a normal genome are differentially labeled and hybridized to a physical representation of the normal genome. The ratio of the hybridization signals at a locus then provides information on the relative copy number in the two genomes. Initially metaphase chromosomes were used for the hybridization target, allowing copy number variations to be mapped with cytogenetic resolution. Recently a new CGH format employing a microarray of mapped genomic clones as the hybridization target has been developed for analysis of human specimens. Resolution of array CGH is over 100 times better, and the copy number information is more quantitative, than with chromosome CGH. In this proposal, array CGH technology will be developed for use in the analysis of murine models. The arrays for CGH measurements will contain approximately 3000 targets, most likely made from BAC clones distributed at 1 Mb intervals over the genome. These clones are now being selected by the mouse genome project, and each will contain a mapped STS or EST. An ancillary product of our proposed project will be the cytogenetic map information, based on FISH, for these clones so that they will become a general resource for murine cytogenetics. This project will: Implement array CGH for scanning the entire murine genome for DNA copy number variability with 1 Mb resolution. Develop a modified IRS-PCR based array technique for allelotyping interspecific crosses and for allele-specific copy number analysis of tumors from interspecific backcross mice. Apply genome-wide array CGH analysis in a collaboration to produce a set of C57BL/6J mice containing a comprehensive set of deletions covering the entire genome. Collaborate with others in the MMHC in the analysis of tumors in mouse models and in the transfer of array CGH capability to the other laboratories. Develop a Web- accessible database and appropriate data interpretation tools for murine array CGH results. In summary, tools to be develop in this project will permit genome-wide, high throughput analysis of DNA copy number in the mouse. Availability of this technique will facilitate genetic and functional studies of mouse models.